Beacon Designer™ supports the Scorpions® chemistry for real time detection of a target sequence. The Scorpions® primers designed are free from dimers, runs, repeats and have a melting temperature within a user specified range.
Beacon Designer™ automatically selects a stem of appropriate length for optimal Scorpions® Tm. You can design specific and efficient Scorpions® by automatically avoiding regions of significant cross homology and by avoiding regions on the template that are susceptible to folding. Beacon Designer™ graphically displays the alternate structures of the designed Scorpions® along with their properties. Alternate structures may lead to false positives or reduce the efficiency of the assay.
Using Beacon Designer™, you can also evaluate pre-designed Scorpions® assays. Pre-designed primer sets can be evaluated or primers for a pre-designed probe can be designed.
Beacon Designer™ automates the design of real time primers and probes. It is used by molecular biologists worldwide to design successful real time PCR assays. It saves the time and the money involved in failed experiments. Beacon Designer™ is a flexible solution to your real time primer and probe design needs and pays for itself many times over.
You can BLAST search sequences and search for template structures from within the program. The results of both these searches are used while designing primers and probes. The regions that exhibit significant cross homologies and template structures are avoided automatically during the design.